
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   29 (  240),  selected   29 , name one
# Molecule2: number of CA atoms   81 (  640),  selected   29 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      59_B - 80_B        4.87    12.78
  LCS_AVERAGE:     25.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      64_B - 80_B        1.83    15.63
  LCS_AVERAGE:     18.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      66_B - 80_B        0.62    16.55
  LCS_AVERAGE:     16.05

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   29
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     V    52_B     V    52_B      3   13   18      0    3    3    3    3    6    9   13   13   15   15   17   17   17   17   17   18   18   20   20 
LCS_GDT     R    53_B     R    53_B     12   13   18      8   11   12   12   12   12   12   13   14   15   15   17   17   17   17   17   18   18   20   20 
LCS_GDT     R    54_B     R    54_B     12   13   18      8   11   12   12   12   12   12   13   14   15   15   17   17   17   17   17   18   18   20   20 
LCS_GDT     A    55_B     A    55_B     12   13   18      8   11   12   12   12   12   12   13   14   15   15   17   17   17   17   17   18   18   20   20 
LCS_GDT     F    56_B     F    56_B     12   13   18      8   11   12   12   12   12   12   13   14   15   15   17   17   17   17   17   18   18   20   20 
LCS_GDT     D    57_B     D    57_B     12   13   18      8   11   12   12   12   12   12   13   14   15   15   17   17   17   17   17   18   18   20   20 
LCS_GDT     L    58_B     L    58_B     12   13   18      8   11   12   12   12   12   12   13   14   15   15   17   17   18   19   20   22   23   23   23 
LCS_GDT     V    59_B     V    59_B     12   13   22      8   11   12   12   12   12   12   13   14   15   15   17   17   17   19   20   22   23   23   23 
LCS_GDT     R    60_B     R    60_B     12   13   22      8   11   12   12   12   12   12   13   14   15   15   17   17   18   19   21   22   23   23   23 
LCS_GDT     E    61_B     E    61_B     12   13   22      8   11   12   12   12   12   12   13   14   15   15   17   17   19   20   21   22   23   23   23 
LCS_GDT     L    62_B     L    62_B     12   13   22      5   11   12   12   12   12   12   14   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     L    63_B     L    63_B     12   13   22      5   11   12   12   12   13   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     P    64_B     P    64_B     12   17   22      5    9   12   12   12   14   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     A    65_B     A    65_B      5   17   22      5    5    5    8   10   13   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     K    66_B     K    66_B     15   17   22      7   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     A    67_B     A    67_B     15   17   22      7   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     E    68_B     E    68_B     15   17   22      7   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     I    69_B     I    69_B     15   17   22      7   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     I    70_B     I    70_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     D    71_B     D    71_B     15   17   22      7   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     A    72_B     A    72_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     L    73_B     L    73_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     R    74_B     R    74_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     E    75_B     E    75_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     E    76_B     E    76_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     A    77_B     A    77_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     E    78_B     E    78_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     K    79_B     K    79_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_GDT     Y    80_B     Y    80_B     15   17   22     10   15   15   15   15   15   17   18   18   18   19   19   19   19   20   21   22   23   23   23 
LCS_AVERAGE  LCS_A:  20.32  (  16.05   18.94   25.97 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_AT     10     15     15     15     15     15     17     18     18     18     19     19     19     19     20     21     22     23     23     23 
GDT PERCENT_AT  12.35  18.52  18.52  18.52  18.52  18.52  20.99  22.22  22.22  22.22  23.46  23.46  23.46  23.46  24.69  25.93  27.16  28.40  28.40  28.40
GDT RMS_LOCAL    0.32   0.62   0.62   0.62   0.62   0.62   1.83   2.12   2.12   2.12   2.83   2.83   2.83   2.83   3.76   4.37   5.08   5.40   5.40   5.40
GDT RMS_ALL_AT  17.02  16.55  16.55  16.55  16.55  16.55  15.63  15.22  15.22  15.22  14.36  14.36  14.36  14.36  13.60  13.19  12.30  12.07  12.07  12.07

# Checking swapping
#   possible swapping detected:  F    56_B      F    56_B
#   possible swapping detected:  E    61_B      E    61_B
#   possible swapping detected:  D    71_B      D    71_B
#   possible swapping detected:  E    75_B      E    75_B
#   possible swapping detected:  E    78_B      E    78_B
#   possible swapping detected:  Y    80_B      Y    80_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V    52_B      V    52_B    37.687     0    0.148   1.012    39.438    0.000    0.000
LGA    R    53_B      R    53_B    34.441     0    0.605   0.902    38.695    0.000    0.000
LGA    R    54_B      R    54_B    32.265     0    0.077   1.493    36.454    0.000    0.000
LGA    A    55_B      A    55_B    27.634     0    0.034   0.047    29.860    0.000    0.000
LGA    F    56_B      F    56_B    24.566     0    0.041   1.150    26.485    0.000    0.000
LGA    D    57_B      D    57_B    23.386     0    0.025   0.957    28.534    0.000    0.000
LGA    L    58_B      L    58_B    19.703     0    0.085   1.075    24.836    0.000    0.000
LGA    V    59_B      V    59_B    14.598     0    0.028   0.899    18.266    0.000    0.000
LGA    R    60_B      R    60_B    13.370     0    0.033   1.400    15.471    0.000    0.000
LGA    E    61_B      E    61_B    14.131     0    0.109   0.880    21.741    0.000    0.000
LGA    L    62_B      L    62_B     9.834     0    0.036   0.992    14.484    6.905    3.512
LGA    L    63_B      L    63_B     4.474     0    0.557   1.438     7.591   37.738   24.821
LGA    P    64_B      P    64_B     3.658     0    0.023   0.297     6.014   50.595   38.844
LGA    A    65_B      A    65_B     3.470     0    0.100   0.098     4.235   50.119   47.524
LGA    K    66_B      K    66_B     2.383     0    0.318   0.625     5.238   67.024   50.106
LGA    A    67_B      A    67_B     1.554     0    0.048   0.051     1.715   72.857   74.571
LGA    E    68_B      E    68_B     1.769     0    0.021   0.968     3.306   70.833   71.323
LGA    I    69_B      I    69_B     2.307     0    0.087   1.048     5.349   66.786   52.381
LGA    I    70_B      I    70_B     1.903     0    0.031   0.134     2.357   70.833   67.798
LGA    D    71_B      D    71_B     1.344     0    0.053   0.335     1.737   81.429   80.357
LGA    A    72_B      A    72_B     1.427     0    0.022   0.047     1.427   81.429   81.429
LGA    L    73_B      L    73_B     1.123     0    0.101   1.401     4.689   88.333   71.667
LGA    R    74_B      R    74_B     1.175     0    0.054   0.871     3.206   83.690   74.805
LGA    E    75_B      E    75_B     0.463     0    0.062   0.531     2.302   97.619   84.921
LGA    E    76_B      E    76_B     0.721     0    0.110   1.152     4.728   90.595   71.587
LGA    A    77_B      A    77_B     1.183     0    0.040   0.044     1.857   81.548   81.524
LGA    E    78_B      E    78_B     1.255     0    0.107   0.696     1.540   81.429   82.487
LGA    K    79_B      K    79_B     1.403     0    0.106   0.848     2.815   81.429   76.878
LGA    Y    80_B      Y    80_B     1.843     0    0.573   1.274     3.745   59.762   60.714

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       29     116    116  100.00     240    240  100.00                81
SUMMARY(RMSD_GDC):     9.981          9.662                 11.449           16.308   14.781

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   29   81    4.0     18    2.12    21.296    20.461     0.810

LGA_LOCAL      RMSD:   2.123  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.222  Number of assigned atoms:   29 
Std_ASGN_ATOMS RMSD:   9.981  Standard rmsd on all 29 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.318142 * X  +  -0.614401 * Y  +   0.722009 * Z  +  20.536901
  Y_new =  -0.856730 * X  +   0.139790 * Y  +   0.496460 * Z  + -36.434589
  Z_new =  -0.405956 * X  +  -0.776511 * Y  +  -0.481903 * Z  +  76.022980 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.215235  0.418024 -2.126225   [DEG:  -69.6278   23.9510 -121.8237 ]
ZXZ:  2.173158  2.073621 -2.659876   [DEG:  124.5128  118.8098 -152.3997 ]
 
# END of job
